Fig. 4
Association of DNA damage and repair with gene expression and chromatin states. a A total of 602 genes that are highly expressed in liver show higher transcription-coupled repair (in TS) and global repair (in NTS). Expression levels for these genes are also correlated with ChIP-seq signals for histone modification markers (H3K4me1, H3K4me3, H3K27ac, and H3K36me3). b A total of 414 genes that are lowly expressed in liver have lower repair and are characterized by H3K27me3, a marker for gene inactivation. Chromatin accessibility (DNase I hypersensitivity site) is higher for both groups of genes in a and b, indicating a role of chromatin states in transcriptional regulation. Median fold change (fc) between liver and the other organs across all significant genes is included on the upper right corner within each panel. c Whole-genome analysis results of DNA damage and repair in liver, with different genomic annotations. Analysis of repair (left) and damage (right) levels across nine genomic annotations for mouse liver reveals uniform distribution of damage but higher repair in active promotor, CpG island (enriched at transcription start sites), transcription elongation and transition regions in genome
